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Complete Genome Sequence of the Salmonella enterica Serovar Paratyphi A Bacteriophage LSPA1 Isolated in China Weikun Zeng,a,b Pujia Mao,b Yu Hong,c Mengdie Feng,b Zeyang Xu,b Fen Huang,b Shenrong Jingb Medical Faculty, Kunming University, Kunming, Yunnan, Chinaa; Medical Faculty, Kunming University of Science and Technology, Kunming, Yunnan, Chinab; Department of Nuclear Medicine, Kunming General Hospital of Chengdu Military Command, Kunming, Yunnan, Chinac
Received 28 August 2014 Accepted 4 December 2014 Published 15 January 2015 Citation Zeng W, Mao P, Hong Y, Feng M, Xu Z, Huang F, Jing S. 2015. Complete genome sequence of the Salmonella enterica serovar Paratyphi A bacteriophage LSPA1 isolated in China. Genome Announc 3(1):e01011-14. doi:10.1128/genomeA.01011-14. Copyright © 2015 Zeng et al. This is an open-access article distributed under the terms of the Creative Commons Attribution 3.0 Unported license. Address correspondence to Weikun Zeng, [email protected].
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aratyphoid fever outbreaks sharply increased in recent years in Asia (1, 2), and its antibiotic resistance is also increasing (3, 4). Understanding Salmonella enterica serovar Paratyphi A phages is important for extending our knowledge and use of phage therapy. The strictly lytic phage LSPA1 was isolated from hospital sewage in Kunming, Southwest China, using the violent strain CMCC50973 of Salmonella Paratyphi A as the host. According to the morphological analysis by transmission electron microscopy, LSPA1 was classified under the family Siphoviridae. DNA sequencing was performed using the Sanger method, with 8⫻ coverage, at the Beijing Genomics Institute (BGI) (Shenzhen, China) using an ABI3700xl automatic sequencer. The sequences were assembled using DNAStar Lasergene version 7.1 (5). LSPA1 contains 41,880 bp and has a G⫹C content of 49.7%. The potential coding sequences (CDSs) were initially annotated using Glimmer (6) and GeneMark (7). The predicted proteins were analyzed using BLASTp (8). The genome contains 58 predicted genes, with an average gene length of about 653 bp. Thirty-eight of the genes are rightward oriented, while the others are leftward oriented. Fifty-three coding sequences begin with the start codon AUG, while three begin with the start codon GUG and two with UUG. Based on the predictions, this phage genome contains genes for phage replication, structure, and lysis. Open reading frames (ORFs) were found for putative homing endonuclease, helicase, and DNA polymerase (locus tags LSPA1_03, LSPA1_34, and LSPA1_40, respectively). The ORFs for terminase, head morphogenesis protein, putative tail protein, and tail fiber protein were found (locus tags LSPA1_03, LSPA1_05, and LSPA1_06, LSPA1_31, respectively). No lysogenization, such as site-specific integrases and repressors, was identified. The ORFs for holin and endolysin were found (locus tags LSPA1_52 and LSPA1_53, respectively). Five phages closely related to LSPA1 are Salmonella phages FSL SP-101 (GenBank accession no. KC139511), wksl3 (GenBank accession no. JX202565), SETP13 (GenBank accession no.
January/February 2015 Volume 3 Issue 1 e01011-14
KF562864), vB_SenS-Ent3 (GenBank accession no. HG934470), and vB_SenS-Ent2 (GenBank accession no. HG934469). Nucleotide sequence accession number. The complete genome of the Salmonella Paratyphi A bacteriopage LSPA1 has been deposited in GenBank under the accession no. KM272358. ACKNOWLEDGMENTS This study was supported by grants from the National Natural Science Foundation of China (no. 31160193) and the Natural Science Foundation of Yunnan Province of China (no. 2012FB135).
REFERENCES 1. Dong BQ, Yang J, Wang XY, Gong J, von Seidlein L, Wang ML, Lin M, Liao HZ, Ochiai RL, Xu ZY, Jódar L, Clemens JD. 2010. Trends and disease burden of enteric fever in Guangxi province, China, 1994 –2004. Bull World Health Organ 88:689 – 696. http://dx.doi.org/10.2471/ BLT.09.069310. 2. Acharya D, Bhatta DR, Malla S, Dumre SP, Adhikari N, Kandel BP. 2011. Salmonella enterica serovar Paratyphi A: an emerging cause of febrile illness in Nepal. Nepal Med Coll J 13:69 –73. 3. Hume S, Schulz T, Vinton P, Korman T, Torresi J. 2009. Increasing rates and clinical consequences of nalidixic acid-resistant isolates causing enteric fever in returned travelers: an 18-year experience. Eur J Clin Microbiol Infect Dis 28:963–970. http://dx.doi.org/10.1007/s10096-009-0732-6. 4. Gupta V, Kaur J, Chander J. 2009. An increase in enteric fever cases due to Salmonella paratyphi A in & around Chandigarh. Indian J Med Res 129: 95–98. 5. Burland TG. 2000. DNASTAR’s Lasergene sequence analysis software. Methods Mol Biol 132:71–91. http://dx.doi.org/10.1385/1-59259-192-2:71. 6. Delcher AL, Bratke KA, Powers EC, Salzberg SL. 2007. Identifying bacterial genes and endosymbiont DNA with Glimmer. Bioinformatics 23: 673– 679. http://dx.doi.org/10.1093/bioinformatics/btm009. 7. Besemer J, Lomsadze A, Borodovsky M. 2001. GeneMarkS: a self-training method for prediction of gene starts in microbial genomes. Implications for finding sequence motifs in regulatory regions. Nucleic Acids Res 29: 2607–2618. http://dx.doi.org/10.1093/nar/29.12.2607. 8. Altschul SF, Madden TL, Schaffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ. 1997. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 25:3389 –3402. http:// dx.doi.org/10.1093/nar/25.17.3389.
Genome Announcements
genomea.asm.org 1
Downloaded from http://genomea.asm.org/ on September 11, 2015 by guest
The bacteriophage LSPA1 was isolated from hospital sewage (Kunming, China), and lytic activity was demonstrated against the Salmonella enterica serovar Paratyphi A CMCC50973 strain. This bacteriophage has a 41,880-bp double-stranded DNA (dsDNA) genome encoding 58 coding sequences (CDSs) and belongs to the family Siphoviridae.
Complete Genome Sequence of the Salmonella enterica Serovar Paratyphi A Bacteriophage LSPA1 Isolated in China Weikun Zeng,a,b Pujia Mao,b Yu Hong,c Mengdie Feng,b Zeyang Xu,b Fen Huang,b Shenrong Jingb Medical Faculty, Kunming University, Kunming, Yunnan, Chinaa; Medical Faculty, Kunming University of Science and Technology, Kunming, Yunnan, Chinab; Department of Nuclear Medicine, Kunming General Hospital of Chengdu Military Command, Kunming, Yunnan, Chinac
Received 28 August 2014 Accepted 4 December 2014 Published 15 January 2015 Citation Zeng W, Mao P, Hong Y, Feng M, Xu Z, Huang F, Jing S. 2015. Complete genome sequence of the Salmonella enterica serovar Paratyphi A bacteriophage LSPA1 isolated in China. Genome Announc 3(1):e01011-14. doi:10.1128/genomeA.01011-14. Copyright © 2015 Zeng et al. This is an open-access article distributed under the terms of the Creative Commons Attribution 3.0 Unported license. Address correspondence to Weikun Zeng, [email protected].
P
aratyphoid fever outbreaks sharply increased in recent years in Asia (1, 2), and its antibiotic resistance is also increasing (3, 4). Understanding Salmonella enterica serovar Paratyphi A phages is important for extending our knowledge and use of phage therapy. The strictly lytic phage LSPA1 was isolated from hospital sewage in Kunming, Southwest China, using the violent strain CMCC50973 of Salmonella Paratyphi A as the host. According to the morphological analysis by transmission electron microscopy, LSPA1 was classified under the family Siphoviridae. DNA sequencing was performed using the Sanger method, with 8⫻ coverage, at the Beijing Genomics Institute (BGI) (Shenzhen, China) using an ABI3700xl automatic sequencer. The sequences were assembled using DNAStar Lasergene version 7.1 (5). LSPA1 contains 41,880 bp and has a G⫹C content of 49.7%. The potential coding sequences (CDSs) were initially annotated using Glimmer (6) and GeneMark (7). The predicted proteins were analyzed using BLASTp (8). The genome contains 58 predicted genes, with an average gene length of about 653 bp. Thirty-eight of the genes are rightward oriented, while the others are leftward oriented. Fifty-three coding sequences begin with the start codon AUG, while three begin with the start codon GUG and two with UUG. Based on the predictions, this phage genome contains genes for phage replication, structure, and lysis. Open reading frames (ORFs) were found for putative homing endonuclease, helicase, and DNA polymerase (locus tags LSPA1_03, LSPA1_34, and LSPA1_40, respectively). The ORFs for terminase, head morphogenesis protein, putative tail protein, and tail fiber protein were found (locus tags LSPA1_03, LSPA1_05, and LSPA1_06, LSPA1_31, respectively). No lysogenization, such as site-specific integrases and repressors, was identified. The ORFs for holin and endolysin were found (locus tags LSPA1_52 and LSPA1_53, respectively). Five phages closely related to LSPA1 are Salmonella phages FSL SP-101 (GenBank accession no. KC139511), wksl3 (GenBank accession no. JX202565), SETP13 (GenBank accession no.
January/February 2015 Volume 3 Issue 1 e01011-14
KF562864), vB_SenS-Ent3 (GenBank accession no. HG934470), and vB_SenS-Ent2 (GenBank accession no. HG934469). Nucleotide sequence accession number. The complete genome of the Salmonella Paratyphi A bacteriopage LSPA1 has been deposited in GenBank under the accession no. KM272358. ACKNOWLEDGMENTS This study was supported by grants from the National Natural Science Foundation of China (no. 31160193) and the Natural Science Foundation of Yunnan Province of China (no. 2012FB135).
REFERENCES 1. Dong BQ, Yang J, Wang XY, Gong J, von Seidlein L, Wang ML, Lin M, Liao HZ, Ochiai RL, Xu ZY, Jódar L, Clemens JD. 2010. Trends and disease burden of enteric fever in Guangxi province, China, 1994 –2004. Bull World Health Organ 88:689 – 696. http://dx.doi.org/10.2471/ BLT.09.069310. 2. Acharya D, Bhatta DR, Malla S, Dumre SP, Adhikari N, Kandel BP. 2011. Salmonella enterica serovar Paratyphi A: an emerging cause of febrile illness in Nepal. Nepal Med Coll J 13:69 –73. 3. Hume S, Schulz T, Vinton P, Korman T, Torresi J. 2009. Increasing rates and clinical consequences of nalidixic acid-resistant isolates causing enteric fever in returned travelers: an 18-year experience. Eur J Clin Microbiol Infect Dis 28:963–970. http://dx.doi.org/10.1007/s10096-009-0732-6. 4. Gupta V, Kaur J, Chander J. 2009. An increase in enteric fever cases due to Salmonella paratyphi A in & around Chandigarh. Indian J Med Res 129: 95–98. 5. Burland TG. 2000. DNASTAR’s Lasergene sequence analysis software. Methods Mol Biol 132:71–91. http://dx.doi.org/10.1385/1-59259-192-2:71. 6. Delcher AL, Bratke KA, Powers EC, Salzberg SL. 2007. Identifying bacterial genes and endosymbiont DNA with Glimmer. Bioinformatics 23: 673– 679. http://dx.doi.org/10.1093/bioinformatics/btm009. 7. Besemer J, Lomsadze A, Borodovsky M. 2001. GeneMarkS: a self-training method for prediction of gene starts in microbial genomes. Implications for finding sequence motifs in regulatory regions. Nucleic Acids Res 29: 2607–2618. http://dx.doi.org/10.1093/nar/29.12.2607. 8. Altschul SF, Madden TL, Schaffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ. 1997. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 25:3389 –3402. http:// dx.doi.org/10.1093/nar/25.17.3389.
Genome Announcements
genomea.asm.org 1
Downloaded from http://genomea.asm.org/ on September 11, 2015 by guest
The bacteriophage LSPA1 was isolated from hospital sewage (Kunming, China), and lytic activity was demonstrated against the Salmonella enterica serovar Paratyphi A CMCC50973 strain. This bacteriophage has a 41,880-bp double-stranded DNA (dsDNA) genome encoding 58 coding sequences (CDSs) and belongs to the family Siphoviridae.
